title: MYDGF Deficiency Exacerbates Mitotic Catastrophe of Podocytes in Glomerular Disease

city: Jinan, Shandong

first: Ping

last: Zhan

address: School of Basic Medical Sciences, Shandong University  44# Wenhua Xi Road

institute: Shandong University

summary: Podocytes, highly differentiated glomerular epithelial cells, are essential for the maintenance of glomerular filtration barrier. Podocyte dysfunction in podocytes is a major determinant of proteinuric kidney disease. By RNA sequencing analysis in ADR-treated podocytes with or without MYDGF overexpression, we observed the significant changes of genes important in regulating cell cycle in podocytes with ADR treatment.

overall_design: The gene expression of 4 samples from a 24 h Adriamycin (ADR) induced NC-MYDGF or AD-MYDGF podocyte cell line was compared to 4 untreated samples by RNA sequencing.

first: Min


title: Genome-wide occupancy of ZRF1 and BRD4 in neuroblastoma cells.

status: Public on Oct 06 2021

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through integrated proteomics and validating studies, we discovered that ZRF1 and BRD4 form a complex with p113, a novel protein derived from CUX1 circular RNA. To investigate the mechanisms underlying the oncogenic functions of ZRF1 and BRD4, we employed the Illumina Novaseq 6000 as a discovery platform to analyze the genome-wide occupancy of ZRF1 and BRD4 on target genes in human SH-SY5Y cells, while the results were further analyzed with p113-regulated target genes. The results showed that 46 target genes were regulated by transcriptional trimer complex p113/ZRF1/BRD4, especially those involved in metabolic pathway or complex I biogenesis, including ALDH3A1, NDUFA1, and NDUFAF5. Furthermore, we validated the ChIP-seq results by real-time PCR with high identity. Overall, our results provided fundamental information about the genomic enrichment of ZRF1 and BRD4 in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Examination of genome-wide occupancy of two different transcriptional regulators in neuroblastoma cells.

first: Tong

last: Qiangsong

first: Zheng

last: Liduan


title: The small RNA Teg41 is a pleiotropic regulator of virulence and stress response in Staphylococcus aureus

status: Public on Oct 07 2021

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

country: USA

institute: Ohio University

type: Expression profiling by high throughput sequencing

summary: In this study, we further characterize the regulation of the αPSM transcript by Teg41. We show that a single chromosomally integrated copy of Teg41 restores virulence, hemolysis, extracellular vesicle production, and αPSM production in a strain deleted for the 3’ end of Teg41 (Teg41Δ3′ strain). We show that substituting four Teg41 nucleotides in the predicted Teg41- αPSM interaction site abolishes increased hemolysis in a Teg41 overexpression strain. We go on to demonstrte that Teg41 expression influences both the stability and abundance of the αPSM transcript, and, interestingly, that the Teg41Δ3′ strain shows decreased stability in more than 50 transcripts and altered expression levels in over 900 transcripts when compared to wild type S. aureus. Finally, we observe that Teg41 plays a role in S. aureus stress response and that the Teg41Δ3′ strain is more severely attenuated in murine systemic infection than a ∆αPSM strain, indicating that Teg41 regulation reaches beyond the αPSMs. Overall, we show that Teg41 is a unique pleiotropic sRNA in S. aureus that influences several key cellular processes.

overall_design: 24 data sets in total. Three biological replicates for each strain (WT and Teg41delta3' strain) at each timepoint. 4 timepoints, T0, 2.5, 5, and 10 mins after rifampicin addition.

first: Rachel

middle: L

last: Zapf

first: Paul

last: Briaud

first: Emily

middle: C

last: Marino

first: Rebecca

middle: A

last: Keogh

first: Raeven

last: Bastock

first: Hailee

middle: M

last: Sorensen

first: Richard

middle: E

last: Wiemels

middle: K


title: T-bet Suppresses TGF-b-independent Gut-resident Memory CD8+ T Cell Differentiation [RNA-seq]

city: San Antonio

first: Nu

last: Zhang

state: TX

address: 7703 Floyd Curl Drive

institute: University of Texas Health Science Center at San Antonio

summary: TGF-beta signaling is required for the differentiation of gut-resident memory CD8 T cells. Here, we showed that the deficiency of transcription factor T-bet partially rescued the differentiation of TGF-beta receptor deficient gut-resident memory CD8 T cells.

overall_design: Congenically marked naïve P14 TCR transgenic CD8 T cells were adoptively transferred into sex-matched C57BL/6 recipients followed by LCMV Armstrong infection. P14 T cells with different phenotypes were FACS sorted from both spleen and small intestine intraepithelial lymphocyte compartment.

first: Liwen

last: Wang

first: Shruti

last: Mishra

first: Chaoyu

last: Ma


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of circular RNA derived from CUX1 exons (ecircCUX1)

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of public datasets, we identified circular RNA derived from CUX1 exons (ecircCUX1) as a novel driver of NB progression. To investigate the mechanisms underlying the oncogenic functions of ecircCUX1, we employed the BGIseq500 as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of ecircCUX1. The results showed that stable over-expression of ecircCUX1 led to altered expression of 2155 human mRNAs, including 460 up-regulated and 1695 down-regulated genes. Then, we found the possible roles of these differentially regulated mRNAs in selected pathways including lipid metabolic reprogramming, mitochondrial complex I activity, invasion, and metastasis by Bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to ecircCUX1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Total RNA of cells stably transfected with empty vector or ecircCUX1 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on a BGIseq500 platform were performed by Beijing Genomics Institute (BGI-Shenzhen, China), and single end 50 bases reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Liduan

last: Zheng


title: Macrophage CEBPD dependent gene expression

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

summary: RNAseq was performed on wild type, CEBPD knock out and CEBPD transactivation domain deleted RAW264.7 macrophages.

overall_design: RAW cells (CEBPD-WT) were treated with CRISPR guides to delete the transactivation domain of CEBPD (CEBPD-TAD) or to delete CEBPD completely (CEBPD-KO). Three independent clones were subsequently seleceted for RNAseq analysis.


title: Transcriptomic changes following CENP-E partial depletion in normal human fibroblasts

city: Palermo

first: Salvatore

last: Feo

address: Viale delle Scienze, ed 16

department: STEBICEF

country: Italy

institute: University of Palermo

summary: Being CENP-E function restricted to mitosis, its haploinsufficiency has been used to study the induced cell aneuploidy. However, the gene expression profile triggered by CENP-E reduction in normal cells has never been explored. To fill this gap, here we investigated whether a gene network associated with siRNAs-induced CENP-E 50% reduction and consequent aneuploidy exists

overall_design: CENP-E was partially depleted by RNA interference in human primary fibroblasts (IMR90) and high-throughput gene expression profiling by DNA microarrays was done at “early” and “late” timepoints to investigate what gene/networks are engaged by CENP-E reduction

first: Viviana

last: Barra


title: The whole transcriptome expression profiling of human macrophages; comparison between control  and human milk exosomes capsulated oligosaccharides treatment

city: kunming

first: shubai

last: Liu

state: yunnan

address: 132 lanhei road,

institute: kunming institute of botany, chinese academic of science

summary: To discover the  regulatory role of human milk exosomes oligosaccharides, The full cDNA was extracted from human macrophages  and then compared the expression profiles of them to discovery the key features regulated by human milk exosomes extracted oligosaccharides.

overall_design: There are  two groups  cells used for this expression profile comparison:  control and human milk exosomes extracted oligosaccharides treated. The RNA was extracted from well cultured cells using TRIzol reagent, and whole transcriptome gene expression profiling were performed using an Affymetrix Human Gene 1.1 ST  whole transcriptome microarray platform.

first: Yingying

last: He

first: Shubai


title: Effect of neuron-specific short-form ATF6 overexpression on gene expression in the mouse brain

city: Durham

first: Wei

last: Yang

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

summary: One major component of cellular proteome resides in the endoplasmic reticulum (ER), the key organelle for protein biogenesis in the secretory pathway. Disruption of ER proteostasis leads to ER stress, which subsequently activates multiple adaptive stress response pathways, collectedly termed as the unfolded protein response (UPR). One UPR branch is mediated by ATF6 (activating transcription factor 6). Activation of the ATF6 branch generates a transcriptional factor: short form ATF6 (sATF6). Since activation of this UPR branch has been shown to be neuroprotective in brain ischemia/stroke, it is critical to identify what genes are regulated by the sATF6 in neurons in vivo and determine the molecular mechanisms underlying the beneficial effects exerted by this UPR branch. In this study, we performed RNA-Seq analysis on the hippocampus from sATF6 conditional transgenic mice.

overall_design: Compare gene expression between control (Emx-Cre) mice and sATF6 conditional knock-in  (sATF6-KI; Rosa26-sATF6-MER;Emx1-Cre ) mice (n =3).


title: Spermatogonia & Buslfan

city: Clermont-Ferrand

first: David

middle: H

last: VOLLE

address: 28 place Henri Dunant

country: France

institute: INSERM

summary: The goal is to analyze the impact of chemotherapy drug busulfan on spermatogonia

overall_design: 18 samples, either 5 or 4 replicates per condition, controls are DMSO treated cells

last: Volle


title: Alterations in circulating monocytes predict COVID-19 severity and include chromatin modifications still detectable six months after recovery

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: An early analysis of circulating monocytes may be critical for predicting COVID-19 course and its sequelae. In 131 untreated, acute COVID-19 patients at emergency room (ER) arrival, monocytes showed decreased surface molecules expression, including HLA-DR, in association to an inflammatory cytokine status and limited anti-SARS-CoV-2-specific T cell response. These alterations were mostly normalized in post-COVID-19 patients, 6 months after discharge. Acute COVID-19 monocytes transcriptome showed upregulation of anti-inflammatory, tissue repair genes such as BCL6, AREG and IL-10 and increased accessibility of chromatin. Some of these transcriptomic and epigenetic features still remained in post-COVID-19 monocytes. Importantly, a poorer expression of surface markers and low IRF1 gene transcription in circulating monocytes at ER defined a COVID-19 patients group with impaired SARS-CoV-2-specific T cell response and increased risk of requiring intensive care or dying.  An early analysis of monocytes may be useful for COVID-19 patients stratification and to designing innate immunity-focused therapies.

overall_design: We performed ATAC sequencing using monocytes of Control patients with no Covid-19 infection, Acute Covid-19 or Post Covid-19 infection

first: Alberto

last: Utrero-Rico

first: Cecilia

last: González-Cuadrado

first: Marta

last: Chivite-Lacaba

first: Oscar

last: Cabrera-Marante

first: Rocio

last: Laguna-Goya

first: Patricia

last: Almendro-Vázquez

first: Carmen

last: Díaz-Pedroche

first: Maria

last: Ruiz-Ruigomez

first: Antonio

last: Lalueza

first: María

last: Dolores Folgueira

last: Vázquez

first: Ana

last: Quintas

first: Marcos

last: Berges-Buxeda

first: Moisés

last: Martín-Rodríguez

last: Dopazo

last: Serrano-Hernández

first: José

last: Aguado

first: Estela

last: Paz-Artal


title: Cochlear fibrocyte and osteoblast lineages expressing type 2 deiodinase identified with a Dio2-CreERt2 allele

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary:
Purpose: To define Dio2-expressing cochlear cell types at high resolution in juvenile mice.
Methods: Individual fluorescent cells were isolated by micro-manipulator from dissociated pieces of cochlea from heterozygous Dio2ERt2 mice then used to construct single-cell RNA-seq libraries.
Results: Consensus clustering of 46 cells revealed two major groups representing fibrocyte, and osteoblast lineages
Conclusions: We identify Dio2-expressing fibrocyte and osteoblast lineages

overall_design: Define Dio2-expressing cochlear cell types by high resolution RNA-sequencing of individual fluorescent Dio2-positive cells.

first: Lily

last: Ng

first: Ye

first: Douglas

last: Forrest


title: Expression data from DEGs in human ESCC EC109 cells transfected with empty lentiviral vector (Lv-NC) or lentiviral vector carrying carrying KDM5C specific shRNA (Lv-shKDM5C)

city: Shantou

first: Li

middle: Ming

last: kai

address: Dong Xia

institute: Shantou University

summary:
Expression data from different expressed genes (DEGs) in human esophageal squamous cell carcinoma (ESCC)  EC109 cells transfected with empty lentiviral vector (Lv-NC) or lentiviral vector carrying carrying KDM5C specific shRNA (Lv-shKDM5C)
Lysine demethylase 5C (KDM5C), a member of lncRNAs, has tumor-suppressor properties and is downregulated in the majority of malignancies. KDM5C was found to suppress some sorts of tumors through regulating epithelial mesenchymal transformation,inducing cell cycle arrest,triggering apoptosis and so on.
We used microarrays to investigate the possible regulatory mechanism of KDM5C in ESCC cell line.

overall_design: KDM5C was downregulated with lentivirus vector carrying sh-KDM5C.Hence,EC109 cells harvested from three dishes were divided into two groups: Lv-NC(control group, Control) and Lv-shKDM5C (downregulated-KDM5C group, sh-KDM5C).A DNA microarray was applied to analyze DEGs,accompanied by bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.

first: Ling-Fei

last: Wu

first: Ming-kai

last: Li

first: Zhe


title: Transcriptional Characterization of healthy retina

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

overall_design: MACE RNA sequencing of 6 human healthy retinal specimens (3 central and 3 periphery)

first: Julian

last: Wolf


title: Intestine-specific activation of LXR via low-dose oral administration of GW3965

city: Chuncheon-si

first: Yong-Hyun

last: Han

state: Kangwondo

address: 307-ho, College of Pharmacy, 1, Kangwondaehak-gil

department: College of Pharmacy

country: South Korea

institute: Kangwon National University

summary: Generation of high density lipoprotein (HDL) requires apoA1 and the cholesterol transporter ABCA1. Although the liver generates most HDL in blood, small intestines also can synthesize HDL. However, distinct functions for intestinal HDL are unknown. Here we designed intestine-specific activation of LXR via low-dose administration of GW3965, LXR agonist. The liver status was improved by therapeutics that elevated and depended upon intestinal HDL production via GW3965. Thus, protection of the liver from injury in response to gut-derived signals like LPS is a major function of intestinally synthesized HDL.

overall_design: GW3965 (Sigma-Aldrich) was suspended in 0.5% carboxymethyl cellulose and was orally administered twice weekly at 1 mg/kg/day for the last 5 weeks in the 10-week period following intestinal resection (small bowel resection; SBR) to floxed control and intestine-specific knockout of ABCA1. The liver and ileum tissue was isolated and RNA was isolated by RNeasy Mini Kit (Qiagen). The isolated RNA samples were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

first: Gwendalyn

last: Randolph


title: Transcriptome analysis of memantine-treated Shank2 wild-type and knock-out mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

summary: Shank2 is an excitatory postsynaptic scaffolding protein strongly implicated in autism spectrum disorders (ASD). Shank2-mutant mice with a homozygous deletion of exons 6 and 7 show decreased NMDA receptor (NMDAR) functions and autistic-like behaviors in juvenile (~postnatal day or P21) and adult (> P56) stages that are rescued by NMDAR activation. These mice, however, show an opposite change increased NMDAR functions—at ~P14, and NMDAR suppression by early and chronic memantine treatment during P7–21 prevents NMDAR hypofunction and autistic-like behaviors at juvenile (~P21) and adult (~P56) stages. To explore molecular mechanisms underlying the long-lasting effects of early memantine treatment, we performed RNA-Seq analysis of forebrains from wild-type and Shank2-mutant mice early and chronically treated with vehicle or memantine. Memantine-treated Shank2-mutant mice showed upregulations of chromatin-related genes and downregulations of mitochondria- and ribosome-related genes. In addition, vehicle-treated Shank2-mutant mice showed transcriptomic patterns that are largely opposite to those observed in ASD, as supported by the expression patterns of ASD-risk/related genes and cell-type-specific genes. These patterns, likely representing compensatory changes, were weakened by early memantine treatment. These results suggest that early chronic memantine treatment in Shank2-mutant mice alters chromatin- and mitochondria/ribosome-related gene expressions and weakens anti-ASD transcriptomic patterns.

overall_design: Forebrain transcriptome of memantine-, vehicle-treated Shank2 wild-type and knock-out mice

first: Ye-Eun

last: Yoo

first: Woohyun

first: Hyosang

first: Seungjoon

last: Lee

first: Hyojin

last: Kang


title: Effects of anti-PD-L1 on the testis transcriptomes of C57BL/6 mice

city: Qingdao

first: Luoyang

last: Wang

state: Shandong

address: 308 Ningxia Road

institute: Qingdao University

summary: To explore the mechanisms of the decreased testosterone after anti-PD-L1 treatment in mice, we performed RNAseq transcriptome analysis of the testes of male mice 7 days later post-treatment with anti-PD-L1 or control IgG. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten. Our results show that pathways involved in both lipid transportation and inflammation were obviously affected by anti-PD-L1 treatment.

overall_design: Testis mRNA profiles of C57BL/6 male mice  after twice adminstarion of anti-PD-L1 or  IgG isotype control.


title: Moringa oleifera concentrate as a complementary treatment in triple negative breast cancer

city: Dallas

first: Linda

middle: Anne

last: Gilmore

address: 4600 HARRY HINES BLVD

department: Clinical Nutrition

institute: UT Southwestern Medical Center

summary: Using a rodent xenograft model of triple negative breast cancer (MDA-MB-231 cells), diet induced obesity, and insulin resistance, the aim of this study is to evaluate the effects of moringa (MC) on improving insulin sensitivity and inhibiting angiogenesis as a dual mechanism by which the efficacy of antineoplastic treatment by standard of care chemotherapy is augmented in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: B6/Rag1KO were fed a HFD to induce obesity. There was no-treatment lean control group. MDAMB231 cells were injected at 14 weeks of age and 10 weeks on diet. Cells were allowed engraft and tumors grow. After tumors were >200 mm3 on average, tumor bearing mice on the HFD were randomized to one of 4 groups: 1) High Fat Vehicle, 2), High Fat Chemotherapy, 3) High Fat Moringa Concentrate, 4) High Fat Moringa Concentrate Chemotherapy. The lean tumor bearing mice received no intervention.

first: L

first: Susan

last: Newman

first: Richard

last: Carmouche

first: Jasleen

last: Kaur

first: Elizabeth

middle: R

last: Zunica


title: A comprehensivly analysis of SE -lncRNA /mRNAs differential expression profiles during chondrogenic differentiation of human bone marrow mesenchymal stem cells

city: BEIJING

first: YU

last: JIANG

address: 56 Nanlishi Road

institute: Beijing Children's Hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To clarify the important signaling pathways, SE-lncRNAs, and mRNAs associated with SE-lncRNAs regulating chondrogenic differentiation of BMSCs, we assessed the expression of SE-lncRNAs and mRNAs in three pairs of non-induced and the corresponding induced chondrogenic differentiation human Bone marrow-derived mesenchymal stem cells samples by using Human Super-Enhancer LncRNA Microarray. A total of 77 SE-lncRNAs were identified with 47 SE-lncRNAs upregulated and 30 SE-lncRNAs downregaulated as chondrogenic differentiation. 308 mRNAs were identified with 245 mRNAs upregulated and 63 mRNAs downregulated. Some pathways, such as the focal adhesion, extracellular matrix (ECM)-receptor interaction, TGF-b signaling pathway, and PI3K-Akt signaling pathway, were identified as the key pathways may be involved in the chondrogenic differentiation of BMSCs. Moreover, 5 potentially core regulatory mRNAs (PMEPA1, ENC1, TES, CDK6, ADIRF) and 37 SE-lncRNAs in chondrogenic differentiation were revealed by bioinformatic analysis.

overall_design: Three uninduced and paired induced chondrogenic differentiation 7days were subjected to Arraystar human microarray analysis to determine differentially expressed SE-LncRNAs and mRNA. All experiment procedures were performed following the Arraystar standard protocol.

first: Yu

last: Jiang

first: Chen

last: Zhang

first: Lujue

last: Long

first: Lihua

last: Ge

first: Jing

last: Guo

first: Zhipeng

last: Fan

first: Guoxia

last: Yu


title: Morphological diversity of single neurons in molecularly defined cell types

city: Seattle

first: Hongkui

last: Zeng

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

summary: Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types, yet our knowledge of the diversity of neuronal morphology, in particular distal axon projection patterns, remains limited. To systematically obtain complete single neuron morphology on a brain-wide scale, we established a platform with five major components: sparse labeling, whole-brain imaging, reconstruction, registration, and classification. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions. We identify 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. We further reveal extensive morphological diversity within each of these major types, some of which cluster into more refined morphological subtypes. We analyze this diversity at different levels following a set of generalizable organizational rules governing long-range axonal projections, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. We illustrate how these rules manifest in different projection neuron types. Although clear concordance with transcriptomic profiles is evident at major projection type level, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell level cross-modality studies. Overall, our study provides a systematic demonstration of the crucial need for quantitative description of complete single cell anatomy in cell type classification, as the cell type-specific morphological diversity reveals a plethora of ways different cell types and individual neurons may contribute to the function of their respective circuits.

overall_design: single-cell RNA-seq data from retrogradely labeled neurons (i.e., Retro-seq), including 1,134 retrogradely labeled neurons from SSp, SSs, MOp and MOs that mapped L2/3, L4 and L5 IT subclass, 300 retro-seq cells that mapped to Car3 subclass, and 1,699 non-retro-seq scRNA cells form Car3 subclass used for clustering analysis.

first: Hanchuan

last: Peng

first: Peng

last: Xie

first: Lijuan

last: Liu

first: Xiuli

last: Kuang

first: Yimin

first: Lei

last: Qu

first: Hui

last: Gong

first: Shengdian

first: Anan

last: Li

first: Zongcai

last: Ruan

first: Liya

last: Ding

first: Zizhen

last: Yao

first: Chao

last: Chen

first: Mengya

first: Tanya

last: Daigle

first: Rachel

last: Dalley

first: Zhangcan

first: Yanjun

last: Duan

first: Aaron

last: Feiner

first: Ping

last: He

first: Chris

last: Hill

first: Karla

last: Hirokawa

first: Guodong

last: Hong

last: Huang

first: Sara

last: Kebede

first: Hsien-Chi

last: Kuo

first: Rachael

last: Larsen

first: Phil

last: Lesnar

first: Longfei

first: Qi

first: Xiangning

first: Yaoyao

first: Yuanyuan

first: An

first: Donghuan

last: Lu

first: Stephanie

last: Mok

first: Lydia

last: Ng

first: Thuc

middle: N

last: Nguyen

first: Qiang

last: Ouyang

first: Jintao

last: Pan

first: Elise

last: Shen

last: Song

last: Sunkin

first: Bosiljka

last: Tasic


title: miRNA expression profiling and identification of a miRNA regulator for macrophage polarization in the murine alveolar macrophage cell line MH-S.

city: Guangzhou

first: Qiujie

last: Wang

state: Guangdong

address: No.107 Yan jiang West Road

department: Department of Respiratory Medicine

institute: Sun Yat-sen University Second University Hospital

summary: Using the highly sensitive miRNA array, we screened differentially regulated miRNAs in IL-4-induced M2 macrophages and explored the functions of miR-378a-3p by Gene Ontology and Kyoto Encyclopedia of Genes annotation. Furthermore, the quantitative real-time polymerase chain reaction, western blot and dual luciferase reporter assay results showed that Grb2 is a specific target of miR-378a-3p, which will give new insights in disclosing the mechanism of macrophage polarization.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, IL-4 induced miRNAs expression in murine alveolar macrophage cell line was measured at 48 hours after exposure to 20 ng/mL IL-4. Three independent experiments were performed.

first: Shanping

last: Jiang


title: Genome-wide screening and characterization of Actinobacillus pleuropneumoniae and its ciprofloxacin-resistant mutants

city: Yucheng

first: Bowen

last: Zheng

address: Rm.22,Area 3,Sichuan agricultural University,No.46 Xinkang Road,Yucheng District,Ya'an City,Sichuan

department: Sichuan Agricultural University

institute: Sichuan

summary: Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Actinobacillus pleuropneumoniae and its ciprofloxacin resistance-inducing derivatives.This study aims to explore the mechanism of acquired ciprofloxacin resistance in Actinobacillus pleuropneumoniae.

overall_design: APP strain SC1810 and its ciprofloxacin-resistance mutant

first: Jiafan

first: Xiaoping

last: Ma


title: Newborn infant skin gene expression: Remarkable differences versus adults

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

summary: At birth, human infants are poised to survive in harsh, hostile conditions. An understanding of the state of newborn skin development and maturation is key to the maintenance of health, optimum response to injury, healing and disease. The observational study collected full-thickness newborn skin samples from 27 infants at surgery and compared them to skin samples from 43 adult sites protected from ultraviolet radiation exposure, as the standard for stable, mature skin. Transcriptomics profiling and gene set enrichment analysis were performed. Statistical analysis established over 25,000 differentially regulated probe sets, representing 10,647 distinct genes, in infant skin compared to adult skin. Gene set enrichment analysis showed a significant increase in 143 biological processes (adjusted p < 0.01) in infant skin, versus adult skin samples, including extracellular matrix (ECM) organization, cell adhesion, collagen fibril organization and fatty acid metabolic process. The top two biological processes were ECM organization and ECM structure organization. Genes involving epidermis development, immune function, cell differentiation, and hair cycle were overexpressed in adults, representing 101 significantly enriched biological processes (adjusted p < 0.01). The top processes involved skin and epidermal development, e.g., keratinocyte differentiation, keratinization and cornification intermediate filament cytoskeleton organization and hair cycle. Over half of the enriched biological processes also involved immune function, including antigen processing and presentation. The results provide essential insight regarding newborn infant skin and its ability to support the newborn’s preparedness to survive and flourish, despite the infant’s new environment laden with microbes, high oxygen tension and potential irritants. To our knowledge, this is the first report on newborn infant skin transcriptomics analysis. When compared to ultraviolet radiation protected adult skin, it highlights the substantial differences between them. This fundamental knowledge is expected to guide strategies to protect and preserve the features of unperturbed, young skin.

overall_design: 70 total skin biopsies analyzed: 27 newborn baby (from a variety of locations) and 43 adult buttock samples. Multiple comparisons are made between newborn and adult skin.

middle: P


title: Transcriptional Characterization of healthy lacrimal gland

first: Clemens

last: Lange

overall_design: MACE RNA sequencing of 8 human healthy lacrimal gland specimens.

first: Julian

last: Wolf


title: Transcriptional profiles of cone cells, rod cells, and pineal photoreceptor cells in zebrafish

city: Bunkyo-ku

first: Daisuke

last: Kojima

state: Tokyo

address: 7-3-1 Hongo

department: Department of Biological Sciences, School of Science

country: Japan

institute: The University of Tokyo

summary: For isolation of rod, cone, and pineal photoreceptor cells, we used the transgenic zebrafish lines, Tg(rho:egfp)ja2Tg, Tg(gnat2:egfp)ja23Tg, and Tg(exorh:EGFP)ja1Tg, which express EGFP in rods, all cone subtypes, and pineal rod cells, respectively. Retinas were dissected from dark-adapted adult fish under dim red light. The isolated retinas were digested with trypsin in Ca2+-free Ringer’s solution. The reaction was terminated by adding soybean trypsin inhibitor and fetal bovine serum. The dissociated EGFP-positive cells were isolated with a fluorescence activating cell sorter (FACSAria, BD Biosciences) by the following three parameters: forward scatter, side scatter and green fluorescence. Goal was to determine differentially expressed genes among three types of photoreceptor cells.

overall_design: Three-condition experiment: cone, rod, and pineal cells. Two biological replicates for each purified cells


title: imPlatelet classifier: Image-converted RNA biomarker profiles enable blood-based cancer diagnostics

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary:
Abstract: Sequencing technologies have enabled in-depth analysis of liquid biopsies in cancer, offering a minimally invasive sample collection. The most widely used material is blood which, next to circulating tumor cells and circulating tumor DNA, is the source of tumor-educated platelets (TEPs).
Methods:  We developed imPlatelet method which converts RNA-sequenced platelet data to images, additionally implementing biological knowledge from the Kyoto Encyclopedia of Genes and Genomes Pathway. First, we tested imPlatelet method on a cohort of 401 non-small cell lung cancer patients and 62 sarcoma patients. Next, we applied the developed tool to platelets collected from a new, independent cohort of 28 ovarian cancer patients and 30 non-cancer benign gynaecological conditions.
Results: imPlatelet provided excellent discrimination between cancer cases and healthy controls, with accuracy equal to 1 in training, validation and independent datasets. When discriminating between ovarian cancer cases and benign conditions, imPlatelet reached 0.91 balanced accuracy, with sensitivity and specificity equal to 0.95 and 0.88, respectively, in an independent test set.  ImPlatelet outperformed current state-of-the-art method thromboSeq in the aspects of balanced classification accuracy, the computational power needed, user experience, and execution time.
Conclusions: According to our knowledge, this is the first study implementing an image-based deep learning approach combined with biological knowledge to classify human samples. Our results on classification of ovarian cancer considerably outperform previously published methods and our own alternative attempts of discrimination. We show that a deep learning image-based classifier accurately identifies cancer, despite the limited number of samples and even among non-cancer conditions which affect platelet transcriptome making the diagnosis difficult.

overall_design: RNA-seq of Tumor-educated platelets in ovarian carcinoma

first: Krzysztof

last: Pastuszak

first: Anna

last: Supernat


title: Genetic landscape of T cells identifies synthetic lethality for T-ALL

first: Connor

last: O'Meara

address: Stuebeweg

institute: MPI

summary: We conducted a ENU forward genetic screen in zebrafish; identifying 42 genes differentially regulating rag1-expressing T cells fitness relative to growth hormone-expressing somatotrophic epithelials. Our forward genetic screens in zebrafish for recessive mutations affecting early T cell development revealed several major genetic pathways. Genes encoding proteins required for DNA repair & replication, cell cycle regulation, pre-mRNA processing, protein processing in the ER, ribosome biogenesis and hematopoiesis were enriched in the collection of mutants identified. To examine the molecular consequences of these mutations, bulk RNAseq was conducted on mutant and sibling wildtype embryos at 5 day post-fertilisation.

overall_design:
RNA-Seq was performed on mutant and wt sibling from each zebrafish line (n = 2 – 6). Mutant and sibling wildtype embryos at 5 day post-fertilisation

Please note that
[1] each processed data files were generated from multiple samples (as indicated in the description field in the corresponding samples) and is linked to the corresponding (sibling) *WT1 sample records (exception for IG447_WT5, IY071_Mut1_2 lines).
[2] As each zebrafish line is maintained by outcrossing to wt fish in order to sustain breeding fecundity, fish are likely to be a mixture of different wt strains (as indicated in the sample strain information), but not all will be equal proportions. Thus  wt siblings were included in the analysis to try and correct for this. Researchers should proceed with care if performing any kind of polymorphism analysis as this will likely vary between fish lines.

first: Thomas

last: Boehm


title: Transcriptomic profiling of guinea pigs with NASH and advanced fibrosis

city: Frederiksberg C.

first: Josephine

last: Skat-Rørdam

address: Ridebanevej 9

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: Københavns Universitet

summary: Non-alcoholic steatohepatitis (NASH) is a serious health challenge affecting millions worldwide, and research advances are restricted by the limited availability of preclinical models recapitulating the complex disease etiology and hepatic histopathology. Uniquely, the diet induced guinea pig model develops NASH with fibrosis resembling human histopathology however, no data is available depicting the guinea pig NASH transcriptome. We provide the first high throughput sequencing results on guinea pig NASH with advanced fibrosis. Transcriptomic profiles in guinea pig NASH clearly separated from controls, and pathways involved in fibrosis, inflammation and lipid metabolism were all highly regulated.

overall_design: Transcriptomic analysis was performed on 6 healthy and 6 guinea pigs with fibrotic NASH.

first: David

last: Højland-Ipsen

first: Stefan

last: Seeman

first: Markus

last: Latta

first: Jens

last: Lykkesfeldt

first: Pernille

last: Tveden-Nyborg


title: Colonic mucosal injury responses

city: Herlev

first: Jakob

middle: Benedict

last: Seidelin

address: Borgmester Ib Juuls Vej 1

department: Department of Gastroenterology D

institute: Herlev Hospital, University of Copenhagen

summary: The mechanisms behind acute mucosal injury responses in humans are poorly investigated.We thus examined the acute responses to mucosal barrier injury in humans with and without UC. A standardized mucosal wound extending to the muscularis mucosa layer was inflicted in the sigmoid colon of 6 patients with quiescent UC and 6 control subjects. Macroscopic, microscopic and molecular injury responses were assessed at 24 and 48 hours by repeated high resolution imaging and collection of biopsies across the wounds which were assessed by RNA sequencing.

overall_design: Prospective study of 6 patients with UC in remission and 6 control subjects. Patients had a biopsy taken at 0 h, 24 h, and 48 h.The biopsies at 24 and 48 h were taken across the biopsies taken at 0 h. No replicates vere included.

middle: B

first: Martin

middle: I

last: Bahl

first: Tine

last: Licht

first: Benjamin

last: Mead

first: Jeffrey

last: Karp

middle: V

last: Johansen

first: Lene

last: Riis

first: Marina

last: Galera

first: Anders

last: Woetmann

first: Jacob

middle: T

last: Bjerrum


title: Distinct roles of Haspin in stem cell division and male gametogenesis

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

summary: The atypical protein kinase Haspin phosphorylates Histone H3 at threonine-3 (H3T3ph) during mitosis. H3T3ph creates a docking site for the Chromosomal Passenger Complex at the inner centromere, enabling correction of erratic microtubule-chromosome contacts and preventing chromosome mis-segregation. Surprisingly, Haspin knockout in the mouse does not cause developmental defects, except for testicular anomalies. Therefore, the physiological role of this kinase and the mechanistic significance of H3T3ph are in question. We show here that mouse embryonic stem cells that lack or overexpress Haspin are prone to chromosome misalignment. However, the cell population as a whole maintains the ability to expand and differentiate into multiple lineages. Although not essential for pluripotency, Haspin affects the expression of several testis-specific genes. Furthermore, the H3T3ph mark is detected in under-condensed chromatin domains of haploid spermatids, in cis with lysine/arginine methylation marks. We propose that Haspin controls a compound phospho-methyl switch and regulates testis-specific transcription.

overall_design: RNA sequence analysis of Stem cells lacking or over-expressing Haspin. 3 biological replicates were used for each case

first: Eleftheria

last: Karanika

first: Fani

last: Kiosse

first: Anastasia

last: Christogianni

first: Yiorgos

last: Sfikas

first: Pantelis

last: Topalis

first: Anna

last: Batistatou

first: Apostolos

last: Klinakis

last: Politou

first: Spyros

last: Georgatos


title: Genome-wide transcriptome analysis of SSCs, iGSCs and FGSCs

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use RNA-seq to report the most comprehensive survey to date of Genome-wide transcriptome  in germline stem cells

overall_design: Examination of the Genome-wide transcriptom in 3 cell types.

first: Xiaoyong

last: Li

first: Geng

middle: G

last: Tian


title: Chidamide triggers BTG1-mediated autophagy and reverses the chemotherapy resistance in the relapsed/refractory B cell lymphoma

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: Rituximab/chemotherapy relapsed and refractory B cell lymphoma patients have a poor overall prognosis, and it is urgent to develop novel drugs for improving the therapies of these patients. A new oral histone deacetylase inhibitor, chidamide shows anti-tumor activity by activating the pro-apoptosis pathway in some other hematological malignancies, suggesting its potential application to the relapsed and refractory B cell lymphoma. In this study, we examined the therapeutic effects of chidamide on the cell and mouse models of the rituximab/chemotherapy resistant B cell lymphoma, as well as the primary B cell lymphoma cells. In Raji-4RH and RL-4RH cells, the rituximab/chemotherapy resistant B cell lymphoma cell lines (RRCL), chidamide treatment induced growth inhibition and G0/G1 cell cycle arrest, which were associated with E2F1/2 inactivation and CDK2 degradation. The primary B cell lymphoma cells from Rituximab/chemotherapy relapsed and refractory patients were also very sensitive to chidamide treatment. Interestingly, chidamide triggered the cell death via the autophagy pathway instead of the activation of apoptosis in Raji-4RH and RL-4RH cells, likely due to the lack of the pro-apoptotic proteins in these resistant cells. In the RNA-seq and chromatin immunoprecipitation (ChIP) analysis, we identified BTG1 and FOXO1 as the direct target genes of chidamide, which control the autophagy and cell cycle respectively in RRCL treated with chidamide. Moreover, the combination of chidamide with the chemotherapy drug Cisplatin sensitized the RRCL to growth inhibition in a synergistic manner. Chidamide-Cisplatin combination significantly reduced the tumor burden of a mouse lymphoma model established with engraftment of RRCL. Taken together, our studies provides a theoretic and mechanistic basis for further evaluation of the chidamide-based clinical trial for rituximab/chemotherapy relapsed and refractory B cell lymphoma patients.

overall_design: Raji and Raji-4RH were treated with DMSO or chidamide (3μM) for 24h and then RNA was subjected to RNA-seq analysis.

first: Jichuan

first: Kai

last: Xue

first: Chun

last: Xu

first: Lan

last: Wang


title: Next Generation Sequencing of Ovarian Cancer Cells upon Exposure to Ascites from Wild Type and TG2-/- Mice

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: The goal of this study was to compare signaling pathways in ovarian cancer cells exposed in vitro or in vivo to peritoneal tumor microenvironment of host TG2+/+ vs. TG2-/- mice. For this, we performed NGS-derived transcriptome profiling (RNA-seq) followed by Ingenuity Pathway Analysis (IPA) of ID8 ovarian cancer cells.

overall_design: Two approaches were undertaken: 1. ID8 ovarian cancer cells  were treated in vitro for 5 days with ascites collected from wild type (WT) or TG2-/- mice; 2. ID8 cells were injected intraperitoneally in WT and TG2-/- mice. At the end of tumor growth experiment (day 45), ovarian cancer cells (EpCAM+) were recovered by magnetic cell separation. mRNA profiles were generated by deep sequencing, in duplicate (approach 1) or triplicate (approach 2), using Illumina technology.

first: Livia

last: Sima

first: Hao

last: Huang


title: Genome-wide DNA methylation analysis in SSCs, iGSCs, and FGSCs

type: Methylation profiling by high throughput sequencing

summary: We use MeDIP-seq to report the most comprehensive survey to date of genome-wide DNA methylation in germline stem cells

overall_design: Examination of the genome-wide DNA methylation in 3 cell types.


title: Effective control of neuropathic pain by interrupting C/EBPβ-CLEC7A cross-talk-mediated NLRP3 inflammasome-dependent pyroptosis

status: Public on Oct 05 2021

city: Beijing

first: Wu

last: Dan

address: Dongzhimennei south steet 16

institute: Institute of Chinese Materia Medica，China Academy of Chinese Medical Sciences

summary:
Neuropathic pain (NP) is a complex chronic pain due to the nervous system damage or diseases.During NP development and progression, the neuroinflammation has been observed along the pain pathways from the spinal cord to the thalamus and the parietal cortex. It may be caused by the activation of glial cells, especially microglia, with production of cytokines and other inflammatory mediators within the central nervous system (CNS), especially in  spinal cord.
In this study, we used microarrays to detect the global gene expression in spinal cord of rats in sham group and CCI model group(an animal model of neuropathic pain), and the differentially expressed genes between diseases and control group were obtained.

overall_design: SC tissues (L4-L6) collected from the rats in the Sham and CCI groups (n= 3 per group) on postoperative day 10 were immersed in TRIzol (Invitrogen, CA, USA) and immediately frozen in liquid nitrogen for the whole-genome microarray detection. Microarray experiments were performed using the Affymetrix GeneChip® Rat Gene 2.0 ST Arrays (Affymetrix, Santa Clara, CA) by Shanghai GMINIX Biotechnology Corporation (Shanghai, China).

first: Dan

first: Chunhui

last: Zhao


title: Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non–Muscle-Invasive Bladder Cancer

city: Chapel Hill

first: Xiaohua

last: Gao

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC

summary: Improved risk stratification and predictive biomarkers of treatment response are needed for non–muscle-invasive bladder cancer (NMIBC). Here we assessed the clinical utility of targeted RNA and DNA molecular profiling in NMIBC. We performed RNA-based profiling by NanoString nCounter on non–muscle-invasive bladder cancer (NMIBC) clinical specimens and found that a novel expression signature of an inflamed tumor microenvironment (TME), but not molecular subtyping, was associated with improved recurrence-free survival after bacillus Calmette-Guérin (BCG) immunotherapy. We further demonstrated that immune checkpoint gene expression was not associated with higher recurrence rates after BCG.

overall_design: Gene expression in NMIBC samples was profiled by NanoString nCounter, an RNA quantification platform, from two independent cohorts (n = 28, n = 50).

first: Markia

middle: A

last: Smith

first: Jeffrey

middle: S

last: Damrauer

first: Kyle

last: Roell


title: Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer

first: Huanlong

last: Qin

address: 301 Yan Chang Road

department: Gastrointestinal Surgery

institute: Shanghai Tenth People’s Hospital Affiliated to Tongji University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Targeting androgen receptor phase separation to overcome antiandrogen resistance mediated by "pharmacological condensates"

first: Junhao

last: Hu

address: Build 13, No.100 Kaike Road, Pudong District

institute: Interdisciplinary Research Center of Biology and Chemistry

summary: Analyze the transcriptomic changes of LNCaP upon DMSO, DHT, Enzalutamide(ENZ), ET516 treatment. The DHT treatment induced robust androgen receptor (AR) signaling up-regulation, wheras ENZ and ET516 can significantly restore DHT-induced AR signaling changes.

overall_design: LNCaP cells were treated with 10 μM ET516/ENZ/DMSO (DHT was added 2 hours after the compound)  for 12 hours. Subsequently RNA were extracted and sequencing libraries were prepared for high thourghput sequencing.

first: Jingjing

last: Xie

last: He

first: Qiangang

last: Zheng


title: ATAC-seq of Embronic Hindgut Epithelia from WT mice

first: Wei

last: Gu

address: 51 Rijing Road

department: Beigene Institute

institute: Beigene

summary: The goal of this study is to study the chromatin accessibility signature of embronic hindgut epithelia

overall_design: Intestine epithelium isolated from embronic hindgut

first: Kushal

last: Banerjee

first: Madhurima

last: Saxena

first: Shariq

last: Madha

first: Judith

last: Kraiczy

first: Ramesh

last: Shivdasani


title: Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus

city: Columbus

first: Jose

last: Guirao-Abad

address: 2255 Kenny Rd

department: Emergency Medicine

institute: Ohio State University

summary: Aspergillus fumigatus is a human-pathogenic mold that extracts nutrients from the environment or from host tissues by secreting hydrolytic enzymes. The ability of A. fumigatus to adjust secretion levels in proportion to demand relies on the assistance of the unfolded protein response (UPR), an adaptive stress response pathway that regulates the unique protein-folding environment of the endoplasmic reticulum (ER). The P5-type ATPase Spf1 has recently been implicated in a novel mechanism of ER homeostasis that involves correcting errors in ER-membrane protein targeting. However, the contribution of this protein to the biology of A. fumigatus is unknown. Here, we employed a gene knockout and RNA sequencing strategy to determine the functional role of the A. fumigatus gene coding for the orthologous P5 ATPase SpfA. The data reveal that the spfA gene is induced by ER stress in a UPR-dependent manner. In the absence of spfA, the A. fumigatus transcriptome shifts toward a profile of altered redox and lipid balance, in addition to a signature of ER stress that includes srcA, encoding a second P-type ATPase in the ER. A DspfA deletion mutant showed increased sensitivity to ER stress, oxidative stress, and antifungal drugs that target the cell wall or plasma membrane. The combined loss of spfA and srcA exacerbated these phenotypes and attenuated virulence in two animal infection models. These findings demonstrate that the ER-resident ATPases SpfA and SrcA act jointly to support diverse adaptive functions of the ER that are necessary for fitness in the host environment.

overall_design: ∆spfA vs Parental strain

first: Martin

last: Weichert

first: Ginés

last: Luengo-Gil

first: Sarah

last: Sez Wah Wong

first: Vishukumar

last: Aimanianda

first: Christina

last: Grisham

first: Nikita

last: Malev

first: Shivani

last: Reddy

first: Laura

last: Woollett

first: David

last: Askew


title: scRNA-Seq of Intestine Epithelia (Ileum and Colon) from Satb2-deficient and WT mice

summary: The goal of this study is to study signal cell transcripton level changes after Satb2 gene loss in the colonic epithelium.

overall_design: Intestine epithelium isolated from adult mice

last: Redmond

first: Qiao

last: zhou

first: Xiaofeng

last: huang


title: A Novel Mouse Model of Diffuse Midline Glioma Initiated in Neonatal Oligodendrocyte Progenitor Cells Highlights Cell- of-origin Dependent Effects of H3K27M I

first: Yusuke

last: Tomita

state: Illinois

address: 225 E Chicago Ave Box 18

department: Pediatrics

summary: Diffuse midline glioma (DMG) is a type of lethal brain tumor that develops mainly in children. The majority of DMG harbor the K27M mutation in histone H3. Oligodendrocyte progenitor cells (OPCs) in the brainstem are candidate cells-of-origin for DMG, yet there is no genetically engineered mouse model of DMG initiated in OPCs. Here, we used the RCAS/Tv-a avian retroviral system to generate DMG in Olig2-expressing progenitors and Nestin-expressing progenitors in the neonatal mouse brainstem. PDGF-A or PDGF-B overexpression, along with p53 deletion, resulted in gliomas in both models. Exogenous overexpression of H3.3K27M had a significant effect on tumor latency and tumor cell proliferation when compared with H3.3WT in Nestin+ cells but not in Olig2+ cells. Further, the fraction of H3.3K27M-positive cells was significantly lower in DMGs initiated in Olig2+ cells relative to Nestin+ cells, both in PDGF-A and PDGF-B-driven models, suggesting that the requirement for H3.3K27M is increased when tumorigenesis is initiated in Nestin+ cells.  Therefore, we need to find how the tumorigenic effects of H3.3K27M are more oncogenic in Nestin+ cells than Olig2+ cells.

overall_design: Five independent tumors with H3.3K27M (PaKC) and three independent tumors without H3.3K27M (PaHC) were snap frozen, RNA extracted, and RNAseq analysis was performed (PDGF-A; H3.3K27M; p53 loss vs. PDGF-A; H3.3WT; p53 loss)

first: Oren

middle: J

last: Becher


title: A Novel Mouse Model of Diffuse Midline Glioma Initiated in Neonatal Oligodendrocyte Progenitor Cells Highlights Cell- of-origin Dependent Effects of H3K27M III

summary: Diffuse midline glioma (DMG) is a type of lethal brain tumor that develops mainly in children. The majority of DMG harbor the K27M mutation in histone H3. Oligodendrocyte progenitor cells (OPCs) in the brainstem are candidate cells-of-origin for DMG, yet there is no genetically engineered mouse model of DMG initiated in OPCs. Here, we used the RCAS/Tv-a avian retroviral system to generate DMG in Olig2-expressing progenitors and Nestin-expressing progenitors in the neonatal mouse brainstem. PDGF-B overexpression, along with p53 deletion, resulted in gliomas. Exogenous overexpression of H3.3K27M had a significant effect on tumor latency and tumor cell proliferation when compared with H3.3WT in Nestin+ cells but not in Olig2+ cells. Further, the fraction of H3.3K27M-positive cells was significantly lower in DMGs initiated in Olig2+ cells relative to Nestin+ cells, suggesting that the requirement for H3.3K27M is reduced when tumorigenesis is initiated in Olig2+ cells.  Interestingly, H3K27 trimethylation was decreased with H3.3K27M induction even in Olig2+ cells. Therefore, we need to find if there is transcriptional changes for the tumorigenesis with H3.3K27M in Olig2+ cells.

overall_design: Five independent tumors with H3.3K27M (PaK) and three independent tumors without H3.3K27M (PaH) were snap frozen, RNA extracted, and RNAseq analysis was performed (PDGF-A; H3.3K27M; p53 loss vs. PDGF-A; H3.3WT; p53 loss)


title: CUT&RUN Analysis of Satb2 Binding in Colonic Stem Cells and Differentiated Cells

first: Wei

last: Gu

summary: Understanding satb2 binding difference in colonic stem cells and differentiated cells

overall_design: Isolated colonic Lgr5DTRGFP+(stem cells) and Lgr5DTRGFP- (differentiated cells) by FACS sorting, SATB2 Cut&Run was performed in those two group cells.

first: Hua

last: Wang


title: Chromatin accessibility changes in experimentally-induced basal to squamous cell carcinoma transition (BST)

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

summary: Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST. Alternatively we drive c-FOS to induce BST. In these various experimentally-induced model of BST, we analyze chromatin accessibility profiles upon Ras/MAPK activation and/or TGFb signaling abrogation. We also analyze chromatin accessibility profiles upon c-FOS activation.

overall_design:
RasV12-expressing and/or TGFbR1-kd ASZcells were processed for ATAC-seq. Two biological replicates were sequenced  per treatment group.
ATACseq profiles of ASZ transfected with doxycycline-inducible empty vector (ctrl) or c-FOS containing vector (c-FOS) upon Dox treatment, were generated by deep sequencing, in duplicate, using Illumina NextSeq. The sequence reads that passed quality filters were analyzed using bowtie for alignment and macs2 for peak calling.

first: Francois

last: Kuonen

first: Sadhana

last: Gaddam


title: ChIP-seq of Colonic Intestine Epithelium from Satb2-deficient and WT mice

summary: We use ChIP-seq to understand the genomic binding sites of SATB2 in colonic epithelium and to study the shifting of CDX2 and HNF4A's genomic binding sites after SATB2 loss in colonic epithelium.

overall_design: Intestine epithelium isolated from adult mice. Genotypes include Vil-CreER;SATB2F/F (SATB2KO), Satb2f/f (Wild Type) mice, Vil-CreER;CDX2F/F (CDX2KO) and Vil-CreER;HNF4AF/F (HNF4AKO)

last: Huang

last: Zhou


title: C-FOS-driven basal to squamous cell transition


title: CircSry regulates spermatogenesis by enhancing γH2AX expression via sponging miR138-5p

status: Public on Oct 04 2021

first: Yanze

last: Song

state: Beijing

address: 1 Beichen West Road

institute: Chinese Academy of Sciences,Institute of Zoology

summary: Purpose:To gain a deeper insight into how circSry regulates spermatogenesis in spermatocytes, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by circSry deletion.

overall_design: Total RNA was extracted from primary spermatocytes of circSry KO  mice and Wild-type mice and generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Haoyi


title: Transcriptomics study of a temperature sensitive mutant (E170K, shot2) in CstF77, a subunit of 3' end mRNA maturation complex in Arabidopsis thaliana

city: Amherst

first: Minsoo

last: Kim

state: MA

address: 240 Thatcher Rd. N340B

department: BMB

institute: University of Massachusetts Amherst

summary: To obtain transcriptome-wide effects of shot2 mutation, we performed RNA-Seq analysis of comparing hot1-4 shot2 double mutant with hot1-4 (control with a dominant-negative mutation in HSP101) in the absence and presence of a heat treatment (38 °C/3h). Heat treatment causes transcriptional readthrough events in hot1-4 shot2, specifically in highly heat-induced genes, including the toxic hot1-4 gene. In addition, failure of correct transcript processing leads to reduced accumulation of many HSP RNAs and proteins, suppressing heat sensitivity of the hot1-4 mutant, due to reduction of the toxic mutant HSP101 protein.

overall_design: hot1-4 and hot1-4 shot2 seedlings grown on agar plates until stage 1.02 were treated with or without heat stress at 38 °C for 3h followed by 22 °C for 1h. Three biological replicates each of four sample groups (12 total samples)

first: Elizabeth

last: Vierling


title: T cell stimulation alters the HIV-1 reservoir by differential activation of proviral chromatin

city: Huddinge

first: Peter

last: Svensson

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: The reservoir of latently HIV-1 infected cells is heterogeneous. To achieve an HIV-1 cure the reservoir of activatable proviruses should be removed, whereas permanently silenced proviruses may be tolerated.   We have developed a method to assess the proviral nuclear microenvironment in single cells. Latently HIV-1 infected cells were transduced with a zinc finger protein specifically binding to the HIV-1 promoter, producing a fluorescent signal as the viral transactivator Tat is recruited to the HIV-1 promoter. In these cells we assessed the proviral chromatin composition simultaneously with the proviral activation.   By linking the Tat promoter recruitment to viral activation, we dissected the mechanisms of HIV-1 reactivation and the consequences of HIV-1 production. A pulse of promoter-associated Tat was identified that contrasts to the continuous production of viral proteins. As expected, promoter H3K4me3 led to massive expression of the provirus following T cell stimulation. However, the activation induced cell cycle arrest and death resulted in an expanded surviving cell fraction with proviruses encapsulated in repressive chromatin. Further, this model can be used to reveal mechanisms of action of small molecules. In a proof-of-concept study we determine the effect of CBP/P300-inhibitor GNE049. We found that only active enhancers, associated with H3K4me1 and H3K27ac, efficiently recruit Tat, as GNE049 that specifically inhibits enhancer H3K27ac also depletes promoter Tat. Despite the absence of Tat, HIV-1 latency reversal still occurred.   Single cell assessment of the chromatin composition of the latent HIV-1 proviruses revealed how T cell stimulation modulates the proviral activity and the subsequent fate of the infected cell.

overall_design: Localization of Tat and ZFP3-FLAG proteins in the chromatin of HIV-1 infected cells..

first: Birgitta

last: Lindqvist

first: J


title: ATAC-seq of Intestine Epithelia (Ileum and Colon) from Satb2-deficient and WT mice

summary: The goal of this study is to study the chromatin accessibility signature  after Satb2 gene loss in the colonic epithelium.

first: Pratik

last: Singh

first: Sean

last: Houghton


title: Enhancer Analysis (CUT&RUN) of Intestine Epithelium from Satb2-deficient and WT mice

summary: Understanding the enhancer activity in SATB2 regulates colonic intestine epithelial fate and tissue plasticity.

overall_design: H3K27ac and H3K4Me1 histone modification analysis on intestine epithelium (Ileum and Colon). Genotypes include Vil-CreER;SATB2F/F (SATB2KO) and Satb2f/f (Wild Type).

first: Xiaofeng

first: Qiao


title: Role of YAP in Liver Regeneration After Acetaminophen Overdose

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary:
Overdose of acetaminophen (APAP) is the major cause of acute liver failure in the Western world with very limited treatment options. Previous studies from our groups and others have shown that timely activation of liver regeneration is a critical determinant of transplant-free survival of APAP-induced acute liver failure (ALF) patients.
We used affy microarrays to explore the mechanisms of transcriptional expression in YAP-KO mice after 300mg/kg APAP overdose.

overall_design: Livers were extracted from wildtype and YAP-KO male mice that were fasted for 0 hour time points. Intraperitoneal injection of 300 mg/kg acetaminophen overdose was given to fasted mice and livers were extracted 24 hours after overdose. RNA was extracted from 100 mg of liver tissue and pooled together (n of 3) to be used for microarray analysis.

first: Samikshya

last: Poudel

first: Diego

last: Paine Cabrera

first: Bharat

last: Bhushan

first: Michael

middle: W

last: Manley

first: Sumedha

last: Gunewardena

first: Hartmut

last: Jaeschke

first: Udayan

last: Apte


title: Analysis of the transcriptome of undifferentiated SH-SY5Y neuroblastoma cells following AS3MT knockout with CRISPR/Cas9.

city: Oxford

first: Sam

last: Washer

state: Oxfordshire

address: NDMRB, Roosevelt Drive

department: Centre for Medicines Discovery

country: United Kingdom

institute: University of Oxford

summary: Aims/Hypothesis: AS3MT is a risk gene for schizoprhenia and the role in neuronal cell lines has not been established. Using CRISPR/Cas9 generated two AS3MT knockout lines (B6/C6) and age matched wild type controls (D2/D3) in SH-SY5Y neuroblastoma cells and characterised the transcriptional response following knockout. We carried out two independent sequencing runs, including independent cell culturing, RNA extraction, library prep, and sequencing and identify considerable overlap of differentially expressed genes identifying a robust transcriptional response following AS3MT knockout. We identified a number of genes involved in cellular adhesions, ribosomal function, cell-cell contact, and neuronal development, as well as a significant enrichment of previously associated schizophrenia genes, including ZNF80a and DRD2.

overall_design: Knockout AS3MT SH-SY5Y and an age matched WT control line were cultured in 6 well plates until confluent and RNA extracted. Differential gene expression were performed with DESeq2, and ontology analysis with GOSeq.

first: Robert

last: Flynn

first: Asami

last: Oguro-Ando

first: Eilis

last: Hannon

first: Joe

last: Burrage

first: Aaron

last: Jeffries

first: Jonathan

last: Mill

first: Emma

middle: L

last: Dempster


title: Transcriptional changes in experimentally-induced basal to squamous cell carcinoma transition (BST) [ASZ_cFOS_RNAseq]

first: Anthony

last: Oro

summary: Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST. Alternatively we drive c-FOS to induce BST. Here, we analyze transcriptional profiles upon c-FOS induction.

overall_design: Methods: mRNA profiles of ASZ transfected with doxycycline-inducible empty vector (ctrl) or c-FOS containing vector (c-FOS) upon Dox treatment, were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Homer.

first: Francois

last: Kuonen

first: Sadhana

last: Gaddam


title: 15-Lipoxygenase-2 Deficiency Induces a Dysfunction in Macrophages that can be Restored by Salidroside

city: Nanchong

first: zhengmin

last: xu

address: Fujiang

department: Department of Pharmacy

institute: North Sichuan Medical College

summary: 15-Lipoxygenase-2 (15-LOX-2) is thought to regulate inflammation and immunological function; however, its mechanisms of action are still unclear. Furthermore, it has been reported that salidroside has anti-inflammatory properties, but its role in macrophage function is not yet understood. In this study, we aimed to determine how 15-LOX-2 expression levels affect the function of macrophages and the effect of salidroside on 15-LOX-2-deficient macrophages. We used multiple functional genetic strategies to determine 15-LOX-2 function in macrophages. 15-LOX-2 deficiency promoted phagocytosis and the proliferation of macrophages and impaired their apoptosis. Mechanistically, the expression levels of cyclophilin B (CypB) were upregulated in 15-LOX-2-deficient Ana-1 macrophages, whereas those of caspase-3 were downregulated. Furthermore, RNA-seq analysis showed that inflammation, complement, and TNF-α signaling pathways were all activated in 15-LOX-2-deficient Ana-1 macrophages. Treatment of 15-LOX-2-deficient macrophages with salidroside, a natural product derived from Rhodiola species, effectively reversed the effects of 15-LOX-2 deficiency on caspase-3 and CypB levels, as well as on apoptosis and proliferation. In conclusion, our study shows a newly identified link between 15-LOX-2 deficiency and salidroside in regulating macrophage survival, proliferation, and function. Salidroside may be a promising therapeutic strategy for treating inflammation-related diseases resulting from 15-LOX-2 deficiency.

overall_design: RNA-seq data of 15-LOX-2 deficient Ana-1 macrophage

first: Chunyang

last: Zhou

first: Zhengmin

last: Xu

first: Tingting

last: Li

first: Xi

last: Yong

first: Huling

last: Wen

first: Rong

last: Huang


title: The eIF2 kinase GCN2 directs keratinocyte collective cell migration during wounding by proper coordination of reactive oxygen species and amino acids

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: Indiana

address: 635 Barnhill Drive, MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Here we report total RNA seq on wounded and unwounded NTERT WT and GCN2 KO cells.

overall_design: Total RNA Seq in wounded and unwounded NTERT WT and NTERT GCN2 KO cells

first: Rebecca

middle: R

last: Miles

first: Parth

middle: H

last: Amin

first: Miguel

last: Diaz

first: Jagannath

last: Misra

first: Erica

last: Aukerman

first: Amitava

last: Das

first: Nandini

last: Ghosh

first: Tanner

last: Guith

first: Michael

middle: D

last: Knierman

first: Sashwati

last: Roy

first: Dan

middle: F

last: Spandau


title: IRF4 Haploinsufficiency Impairs Affinity Maturation

city: Davis

first: Monica

last: Britton

address: 451 Health Sciences Dr., Rm. 1300

department: Genome Center Service Cores

institute: University of California, Davis

summary: Single cell RNA seq (scRNA-seq) has emerged as a powerful tool to determine the composition of heterogeneous cell states in a tissue. We found that Irf4+/- antigen specific B cells were functionally impaired in affinity maturation. The goal of this study was to determine whether Irf4+/- antigen specific B cells exhibited distinct cellular composition compared to wild type cells. Sequence data from 8360 cells revealed a similar distribution and numbers of cell states between cells of Irf4+/- or Irf4+/+ genotypes.

overall_design: scRNA-seq of Irf4+/- and Irf4+/+ antigen specific Germinal Center B cells at day 10 of an immune response.

first: Sarah

last: Cook

first: Evelyn

middle: P

last: Sievert

first: Roger

last: Sciammas


title: Rhythmic gene expression in mouse intestinal organoids

city: Windsor

first: Phillip

last: Karpowicz

state: Ontario

address: 401 Sunset Ave

department: Biomedical Sciences

country: Canada

institute: University of Windsor

summary: Circadian rhythms are 24h changes in biochemical, physiological and behavioural processes. When ciricadian rhythm are perturbed, like in shiftwork, lead to negitive health outcomes, such as cancer. We assess circadian transcriptional regulation in healthy (APC+_+) and tumourigenic (APCmin) organoids with (BMAL1_WT) or without (BMAL1_Mut) a functional circadain clock. Our results show that the clock controls several genes involved in stem cell signalling pathways.

overall_design: Gene expression levels were assessed 24-46h after synchronization with dexamethasone using high throughput RNA sequencing. Alleles are APC control (APC_WT), APCmin (APC_MUT), Bmal1 control (BMAL1_WT), and Bmal1 null mutant (BMAL1_MUT).

first: Kyle

last: Stokes

first: John

middle: B

last: Hogenesch

first: Danillo

middle: E

last: Flôres

first: Gang

last: Wu


title: Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis

city: London

first: Adam

last: Byrne

state: London

address: South Kensingtion Campus

department: National Heart and Lung Institute

institute: Imperial College London

type: Methylation profiling by genome tiling array

summary: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the epigenetics of AMs development and influence of disease on these processes remain limited. Using EPIC arrays, we undertook DNA methylation profiling in AMs from Healthy (n=14) and IPF (n=30) donors. Deconvolution using reference myeloid-cell methylomes identified epigenetic heterogeneity was a key characteristic of both AMs and IPF and adjustment for myeloid methylome composition was critical in differential methylation analysis. We identified n=11 and n=49 differentially methylated positions (DMPs) and regions (DMRs) between healthy and IPF AMs respectively. Both DMPs and DMRs encompassed genes involved in lipid (LPCAT1) and glucose (PFKB3) metabolism and processes and pathways pertinent to macrophage biology (e.g. extravasations) and IPF pathogenesis (e.g. wound healing). These data identify that changes in the epigenome underpin the development and function of AMs in the IPF lung.

overall_design: DNA methylation profiling of airway macrophages from IPF and Healthy lungs.

first: P

last: McErlean

first: A

first: C

last: Bell

middle: M

last: Lloyd

first: T

last: Maher


title: Plasma Membrane Integrity Signaling

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

summary: To understand the transcriptional response of mammalian cells to plasma membrane stress we induced partial loss of plasmid membrane integrity by chemogenetic induction of pore forming proteins (Gasderimin and MLKL) or treatment with the detergent digitonin.   We monitored transcription with mRNAseq in the immediate hours after plasma membrane damage and identified conserved transcriptional programs.

overall_design: To induce PM damage that could be tolerated by cells, we fused proteins of human MLKL N-terminal (1-181aa) with a tandem FK506 binding domain of FKBP (Fv) and stably transduced in NIH3T3 cells. We found that the oligomerization of MLKL1-181-2xFv by B/B homodimerizer (AP20187, binds to Fv domains, hereafter referred to as "B/B") initiated PM damage by direct MLKL pore-forming. We determined that 100 nM B/B could lead to sub-lethal membrane damage to most of the cells. Alternatively, the Gasdermin family proteins, including GSDMD, can directly form  PM pores. When GSDMD N-terminal (1-276aa) was fused with hormone-binding domain (HBD*), addition of  4-Hydroxytamoxifen (4-OHT) led to direct plasma membrane damage in the absence of additional signals. Parallel with hMLKL1-181-2xFv, a limited sub-lethal GSDMD (by optimized 4-OHT concentration, such as 50 nM) induced membrane damage elicited a PM damage response. Or, we used digitonin to achieve a sub-lethal PM damage. After sub-lethal PM damage, we performed several RNAseq as below.

first: Yi-Nan

last: Gong


title: RNA-seq of desiccated Cronobacter sakazakii ATCCTM29544 on stainless steel coupons

city: Dublin

first: Yu

last: Cao

address: University College Dublin, Belfield, Dublin 4

country: Ireland

institute: University College Dublin

summary: Cronobacter sakazakii is well-known for its desiccation tolerance in the powdered infant formula (PIF) food production environment and the bacterium has been linked with high fatality rates in neonates who consume contaminated product. In this study, using deep-level RNA-sequencing, differentially expressed genes were studied in C. sakazakii ATCCTM29544 grown in simulated low-moisture environment designed to mimic the PIF production environment. Desiccation of bacteria was carried out on stainless steel coupons from which total RNA was subsequently recovered and sequenced. During 4 h of desiccation from the early stationary phase (ESP) grown culture, an approximately 3 log10 reduction was recorded for C. sakazakii viable cell count, with the largest change in viable cells occurring between desiccation hour 1 and 2 during which the culture medium was completely dried. Transcriptomic data obtained after 4 h of desiccation highlighted several highly-up regulated osmotolerance-related genes which were associated with the secondary response mechanism. These actively expressed genes mainly modulate pathways that synthetize glycine betaine and trehalose as well as the transport of these two and other compatible solutes. Understanding the activities of these genes and pathways will assist the development of technologies that mitigate the survival of C. sakazakii in the PIF production process.

overall_design:
RNA-seq was carried out for C. sakazakii ATCCTM29544 at 7 different growth/desiccation/rehydration stages, duplicate samples were sequenced for each stage

Developmental stages used in this study:
EEP (early exponential phase)
MEP (medium exponential phase)
LEP (late exponential phase)
ESP (early stationary phase)
DP (desiccation phase)
RP (rehydration phase)
LSP (late stationary phase)

first: Sathesh

middle: K

last: Sivasankaran

first: Ankita

last: Naithani

first: Shabarinath

last: Srikumar

first: Séamus

last: Fanning


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and BPA stress human neural stem cells(hNSC) Transcriptomes

status: Public on Oct 03 2021

city: Jinan

first: Qinglu

last: Wang

state: Shandong

address: 10600 Century Avenue

institute: Shandong Sport University

summary: Bisphenol A (BPA) is a common industrial chemical widely used to produce various plastics and is known to impair neural stem cells (NSCs). However, the effects of low-dose BPA exposure on the stemness maintenance and differentiation fate of NSCs remain unclear in the infants brain. Here we demonstrated that 1 μM BPA promoted human NSC proliferation and stemness, and didn’t significantly increase cell apoptosis. The Chip-seq experiments demonstrated that both the cell cycle and the TGF-beta signaling pathway were accelerated under the 1 μM BPA condition.

overall_design: Human neural stem cells mRNA profiles by 1 μM bisphenol A

first: Ying

last: Luo

first: Ganghui

last: Ye

first: Xinzhuo

last: Tu


title: Results of the phase 1, randomized, placebo-controlled first-in-human trial of griffithsin formulated in a carrageenan vaginal gel

city: New York

first: Natalia

last: Teleshova

state: NY

address: 1230 York Avenue

institute: Population Council

summary: Griffithsin (GRFT) is an anti-viral lectin with potent anti-HIV activity. GRFT’s preclinical safety, lack of systemic absorption after topical administration, and lack of cross-resistance with existing products prompted its development for topical HIV pre-exposure prophylaxis. We evaluated safety, pharmacokinetics and pharmacodynamics of PC-6500 (0.1% GRFT in a carrageenan (CG) gel) in healthy, HIV-negative, non-pregnant women following once daily vaginal gel administration for 14 days. No significant adverse events, histopathological changes in cervico-vaginal mucosa, or anti-drug (GRFT) antibodies were detected. No cervicovaginal proinflammatory responses and no changes in the ectocervical transcriptome were evident. Vaginal microbiome remained largely unchanged. Reduced abundance of vaginosis-associated bacteria and decreased levels of proinflammatory chemokines (CXCL8 and CCL20) were observed. GRFT was not detected in plasma. GRFT and GRFT/CG in CVLs dose-dependently inhibited HIV and HPV, respectively, in vitro. The data suggest GRFT/CG is a promising on-demand multipurpose prevention product that warrants further investigation.

overall_design: Ectocervical biopsies from 12 subjects collected before exposure to gel (baseline, BL) and 24h after last gel administration. Total 24 samples.

first: Hong

last: Hur


title: A functional conserved fragment of long intergenic non-coding RNA linc-AhRA negatively regulates innate antiviral response in microglia

city: GuangZhou

first: Yiliang

address: Biomedicine Research and Development Center, Jinan University, Guangzhou 510632, Guangdong, PR China. Tel/fax.: +86 20 85223426.

institute: Jinan University

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify functional lncRNAs in microglia-neurotropic virus interaction, high-throughput RNA sequencing was performed to obtain differential expressed lncRNAs (DELs) in microglia isolated from C57BL/6J mice, infected with or without neurotropic virus herpes simplex virus type 1 (HSV-1) (MOI 1 per group). All samples contain three mice’s microglia as a mixture given the isolated amount is low.

overall_design: Microglia lncRNA profiles of primary microglia with neurotropic virus HSV-1 infection or without

first: Weisheng

first: Lianzhou

last: Huang

first: Yifei


title: Single cell RNA sequencing of healthy human airway epithelia

status: Public on Oct 02 2021

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to compare cell composition and gene expression of different cell types in healthy primary human airway epithelia cultured at the air-liquid interface

overall_design: Well differentiated, primary human airway epithelia at the air liquid interface were dissociated and prepared for single cell sequencing via 10X Genomics Chromium controller, and sequenced on Illumina HiSeq 4000

first: Andrew

last: Thurman


title: SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling

city: Shanghai

first: Wei

last: Gu

address: 51 Rijing Road

institute: Beigene

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 118 (45 in the current release) brain functional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single-cell methylome with single-cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design:
Apply snmC-seq2 to brain functional regions to identify the epigenomic landscape of the adult mouse brain.

The file GSE132489_GEOaccession_with_CEMBA_ID.txt.gz, available at the foot of this record contains all included GSE ID with associated CEMBA ID.

This project includes the following series:
GSE130553 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130553
GSE131192 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131192
GSE131326 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131326
GSE131354 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131354
GSE131360 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131360
GSE131393 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131393
GSE131406 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131406
GSE131427 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131427
GSE131430 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131430
GSE131501 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131501
GSE131509 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131509
GSE131519 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131519
GSE131554 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131554
GSE131557 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131557
GSE131570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131570
GSE131757 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131757
GSE131766 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131766
GSE131771 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131771
GSE131836 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131836
GSE131867 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131867
GSE131889 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131889
GSE131904 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131904
GSE131913 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131913
GSE131930 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131930
GSE131951 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131951
GSE132060 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132060
GSE132101 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132101
GSE132114 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132114
GSE132126 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132126
GSE132135 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132135
GSE132405 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132405
GSE132445 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132445
GSE132456 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132456
GSE132463 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132463
GSE132484 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132484
GSE132498 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132498
GSE132503 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132503
GSE132541 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132541
GSE132571 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132571
GSE132601 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132601
GSE132609 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132609
GSE132621 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132621
GSE132629 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132629
GSE132639 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132639
GSE132676 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132676
GSE132692 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132692
GSE132700 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132700
GSE132710 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132710
GSE134474 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134474
GSE134484 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134484
GSE134490 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134490
GSE134507 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134507
GSE134593 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134593
GSE134617 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134617
GSE134635 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134635
GSE134653 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134653
GSE134750 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134750
GSE134773 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134773
GSE134793 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134793
GSE134806 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134806
GSE134862 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134862
GSE134882 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134882
GSE134899 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134899
GSE134940 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134940
GSE134958 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134958
GSE134967 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134967
GSE135139 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135139
GSE135169 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135169
GSE135179 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135179
GSE135203 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135203
GSE135234 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135234
GSE135248 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135248
GSE135252 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135252
GSE135260 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135260
GSE135269 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135269
GSE135307 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135307
GSE135447 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135447
GSE135484 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135484
GSE135534 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135534
GSE135543 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135543
GSE135570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135570
GSE135585 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135585
GSE135596 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135596
GSE135606 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135606
GSE135641 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135641
GSE156683 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156683
GSE157868 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157868
GSE157886 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157886
GSE157980 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157980
GSE158014 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158014
GSE158043 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158043
GSE158066 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158066
GSE158092 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158092
GSE158154 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158154

first: Hanqing

last: Liu

first: Anna

last: Bartlett

last: Aldridge

first: Chongyuan

first: Jacinta

last: Lucero

last: Nery

first: Julia

last: Osteen

first: Jingtian

last: Zhou

last: Tian

first: Huaming

last: Chen

first: Angeline

last: Rivkin

first: Rosa

middle: G

last: Castanon

first: Antonio

last: Pinto-Duarte

first: Carolyn

last: O'Connor

first: Lara

last: Boggeman

first: Conor

last: Fitzpatrick

first: Margarita

last: Behrens


title: Systematic Functional Characterization of Antisense eRNA of Protocadherin alpha HS5-1 Enhancer

first: Yuxiao

address: Dongchuan Road NO.800

institute: Shanghai Jiaotong University

summary: Enhancers generate bidirectional noncoding enhancer RNAs (eRNA) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5’ capped antisense eRNA PEARL (Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin (Pcdh) alpha HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA-fragment editing, CRISPRi, and CRISPRa as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we find that PEARL regulates Pcdh alpha gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancer and target promoter. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 leads to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdh alpha promoter choice in single cells in the brain.

first: Qiang

last: Wu


title: CTRP3 exacerbates tendinopathy by dysregulating tendon stem cell differentiation and altering extracellular matrix composition [array]

city: Seoul

first: Yongsik

last: Cho

address: 1 Gwanak-ro, Gwanak-gu, Seoul 08826. School of Biological Sciences, SNU

institute: Seoul National Universiy

summary: Tendinopathy, the most common disorder affecting tendons, is characterized by chronic disorganization of the tendon matrix, which eventually leads to tendon tear and rupture. The goal of this study was to identify a rational molecular target whose blockade can serve as a potential therapeutic intervention for tendinopathy. We identified C1q/TNF-related protein-3 (CTRP3) as a markedly upregulated cytokine in human and rodent tendinopathy. Overexpression of CTRP3 enhanced the progression of tendinopathy by accumulating cartilaginous proteoglycans and degenerating collagenous fibers in the mouse tendon, whereas CTRP3 knockdown suppressed the tendinopathy pathogenesis. Functional blockade of CTRP3 using a neutralizing antibody ameliorated overuse-induced tendinopathy of the Achilles and rotator cuff tendons. Mechanistically, CTRP3 elicited a transcriptomic pattern that stimulates abnormal differentiation of tendon stem/progenitor cells (TSPCs) and ectopic chondrification in tendons, as an effect linked to activation of Akt signaling. Collectively, we reveal an essential role for CTRP3 in tendinopathy and propose a potential therapeutic strategy for the treatment of tendinopathy.

overall_design: Transcriptomic analysis using tendons isolated from various mouse tendinopathy models.

first: Hyeon-Seop

last: Kim

first: Jin-Hong


title: Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells

city: Tsurumi-ku, Yokohama

first: Yuki

last: Sakamoto

state: Kanagawa

address: 1-7-22, Suehiro-cho

department: CSRS

institute: RIKEN

summary: Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. Here we show that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated leaf cells in Arabidopsis. We demonstrate that intervention of histone acetyltransferases causes severe defects in callus formation from leaf mesophyll protoplasts. Our data suggest that histone acetylation affects transcription of auxin biosynthesis genes. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for the cell cycle reactivation in protoplasts. These findings provide novel mechanistic insights into how differentiated plant cells revert their fate and reinitiate the cell cycle to exert pluripotency.

overall_design: Expression profiling for fresh and cultured mesophyll protoplasts from Arabidopsis leaves

first: Keiko

last: Sugimoto


title: Transcriptome analysis of apple peel samples at different time points in the process of changing from green to red under light conditions after unbagging

city: Yangling

first: Bo

last: Zhang

state: Shanxi

address: College of Horticulture, Northwest A﹠F University

summary: Purpose:The red coloration of apple (Malus × domestica Borkh.) is due to the accumulation of anthocyanins in the fruit peel. Light is essential for anthocyanin biosynthesis in apple.Apple peel can quickly turn red under light conditions after unbagging. Therefore, the implementation of transcriptome sequencing to find genes that promote anthocyanin accumulation in response to light signals is necessary to clarify the mechanism of light-induced anthocyanin accumulation in apple peel.

overall_design: The peel samples at the following three time-points underwent an RNA-seq analysis: 0 h (G0), 6 h (G6), and 24 h (G24). Three biological replicates are included. A total of nine samples were analyzed.

first: Zhen-Zhen

last: Zhu

first: Hui-Juan

last: Yang

first: Zheng-Yang

last: Zhao